A case of an atypical thyroglossal duct cyst is described in a 9-year-old boy who presented with a lateral neck mass that was hypofunctioning on thyroid scan and clinically indistinguishable from a thyroid nodule. Preoperative fine needle aspiration biopsy results demonstrating abundant, normal appearing squamous epithelial cells and keratinaceous material was suggestive of the diagnosis. Definitive diagnosis was made only after complete mobilization of the left lobe of the thyroid gland and cyst resection. A standard Sistrunk procedure was performed, and cyst excision was accomplished without resection of the left lobe of the thyroid gland. Microscopic examination disclosed a keratinizing pseudostratified squamous epithelium that has not been previously reported with thyroglossal duct cysts.